The formation of neuronal connections requires the precise guidance of developing axons toward their targets. In the Drosophila visual system, photoreceptor neurons (R cells) project from the eye into the brain. These cells are grouped into some 750 clusters comprised of eight photoreceptors or R cells each. R cells fall into three classes: R1 to R6, R7, and R8. Posterior R8 cells are the first to project axons into the brain. How these axons select a specific pathway is not known. Here, we used a microarray-based approach to identify genes expressed in R8 neurons as they extend into the brain. We found that Roundabout-3 (Robo3), an axon-guidance receptor, is expressed specifically and transiently in R8 growth cones. In wild-type animals, posterior-most R8 axons extend along a border of glial cells demarcated by the expression of Slit, the secreted ligand of Robo3. In contrast, robo3 mutant R8 axons extend across this border and fasciculate inappropriately with other axon tracts. We demonstrate that either Robo1 or Robo2 rescues the robo3 mutant phenotype when each is knocked into the endogenous robo3 locus separately, indicating that R8 does not require a function unique to the Robo3 paralog. However, persistent expression of Robo3 in R8 disrupts the layer-specific targeting of R8 growth cones. Thus, the transient cellspecific expression of Robo3 plays a crucial role in establishing neural circuits in the Drosophila visual system by selectively regulating pathway choice for posterior-most R8 growth cones.A striking feature of the insect visual system is the organization of neurons into parallel, interconnected layers and orthogonal columns that contain the axonal and dendritic processes from many neurons (1). Columnar organization preserves the topology of visual space. This organization is achieved, in part, during development by the assembly of axons into discrete fascicles. The fly eye comprises some 750 ommatidia or simple eyes, each containing a cluster of eight photoreceptor neurons (R1-R8). R-cell axons form a topographic map of the visual world in the lamina and medulla. The R1 to R6 axons terminate in the lamina, and R7 and R8 extend through the lamina and terminate in the medulla. Axons from each ommatidium form a discrete fascicle and form connections within columnar units, referred to as cartridges and columns in the lamina and medulla, respectively. The orderly assembly of cartridges and columns relies upon the precise spatiotemporal pattern of R-cell innervation.Two features of early eye development facilitate the orderly assembly of the visual system. First, individual rows of ommatidia are recruited sequentially, following a wave of differentiation beginning at the posterior margin of the eye primordium or eye disk and progressing anteriorly across it. As new ommatidia form, the R cells within them extend axons into the brain. Thus, the wave of ommatidial formation is converted into sequential innervation of the brain (2). Second, R cells in the same developing ommatidium extend axons within a s...